Interacting with NIOS II Processor

depending upon what the rest of the fpga is you have 2 ways to implement that

1. you can create an sopc component that holds the rest as included modules

2. you can create an sopc component that just connects to avalon and holds only those control registers and status registers, but all signals go out of your sopc module to top level and you do those connections there.

both methods have there postive and negative sides.

with both methods you won't need to restart the sopc builder again as long as the avalon interface between avalon switch fabric and your custom ip does not change.